presentation

group 9

Introduction

  • Smoking during pregnancy
  • Dataset from NCBI containing, 37-45 non-smokers and 17-19 smokers
# A tibble: 65 × 18,648
   title    geo_accession smoking_status tissue age_group   age BMI_class parity
   <chr>    <chr>         <chr>          <chr>  <chr>     <dbl> <chr>      <dbl>
 1 non-smo… GSM674181     non-smoker     mater… (20,30]    20.5 Normal w…      1
 2 smoker … GSM674182     smoker         mater… (20,30]    29.8 Overweig…      1
 3 non-smo… GSM674183     non-smoker     mater… (30,40]    31.0 Normal w…      3
 4 non-smo… GSM674184     non-smoker     mater… (30,40]    32.9 Normal w…      3
 5 non-smo… GSM674185     non-smoker     mater… (20,30]    28.1 Normal w…      3
 6 non-smo… GSM674186     non-smoker     mater… (20,30]    28.4 Normal w…      2
 7 non-smo… GSM674187     non-smoker     mater… (30,40]    34.6 Normal w…      4
 8 smoker … GSM674188     smoker         mater… (30,40]    33.5 Obesity …      2
 9 smoker … GSM674189     smoker         mater… (30,40]    34.5 Overweig…      3
10 non-smo… GSM674190     non-smoker     mater… (30,40]    30.6 Normal w…      2
# ℹ 55 more rows
# ℹ 18,640 more variables: gestational_age <dbl>, birth_type <chr>,
#   placental_weight <dbl>, newborn_weight <dbl>, apgar_score <dbl>,
#   cotinine_conc_maternal <dbl>, cotinine_conc_cord <dbl>, individual <dbl>,
#   JMJD1A <dbl>, NCOA3 <dbl>, LOC389834 <dbl>, SPIRE2 <dbl>, C17orf77 <dbl>,
#   NXT2 <dbl>, CHKB <dbl>, E2F5 <dbl>, NTN2L <dbl>, TRAIP <dbl>, CSF3R <dbl>,
#   ARL13A <dbl>, AMDHD1 <dbl>, SDHAP3 <dbl>, FLYWCH1 <dbl>, PSRC2 <dbl>, …

/

Materials and Methods (Data handling)

flowchart TD
  subgraph 01_load
  A[ncbi_data] -->|"write_tsv"| B[01_ncbi_data.tsv.gz]
  I["annotation_data$probes"] --> |"write_tsv"| J["01_ncbi_annot_probes.tsv.gz"]
  end
  subgraph 02_clean
  B[01_ncbi_data.tsv.gz] -->|"read_tsv"| C[ncbi_data]
  C[ncbi_data] -->|"as_tibble |> <br/>filter(!str_detect) |> <br/>slice(41:n) |> <br/>t()"| D[ncbi_dirty_pheno]
  D[ncbi_dirty_pheno] --> |"colnames[1, ] |> <br/>str_replace_all('!sample_', ' ')"| E[ncbi_dirty_pheno]
  E[ncbi_dirty_pheno] --> |"[-1, ] |> <br/>as_tibble() |> <br/>rename_with()"| F[ncbi_dirty_pheno]
  F[ncbi_dirty_pheno] --> |"select() |> <br/>mutate() |> <br/>select() |> <br/>t() |> <br/>as.data.frame() |> <br/>rename_with() |> <br/>as_tibble()"| H[ncbi_clean_pheno]
  
  C[ncbi_data] --> G[ncbi_dirty_expr]
  G[ncbi_dirty_expr] --> |"slice() |>  <br/>colnames() |>  <br/>slice() |>  <br/>unlist()"| L[ncbi_dirty_expr]
  L[ncbi_dirty_expr] --> |"rename() |> <br/>mutate(across(-probe.id, ~ as numeric(.x))) "| M[ncbi_dirty_expr]
  
  
  J["01_ncbi_annot_probes.tsv.gz"] -->|"read_tsv()"| N["ncbi_annot_probes"]
  N["ncbi_annot_probes"] --> |"select()"| O["gene_annotation"]
  
  O["gene_annotation"] ---|"select()"| P( ):::empty
  M["ncbi_dirty_expr"] --- P( )
  P( ) -->|"right_join(by = c('Probe_Id' = 'probe_id')) |> <br/>rename() |> <br/>select()"| Q["ncbi_clean_expression"]
  
  end

Results (some dramatic name)

Association plots

Volcano Plot

Discussion

Group 9 presentation